By Stefan Doerr
Molecular dynamics has matured to the point where users can simulate multiple protein systems over timescales as large as milliseconds (see reference of HTMD and ACEMD at https://www.acellera.com/science/).
However, the preparation of the protein systems remains a complex step.
Tools already exist which allow the preparation of an MD system using visual GUIs or webservers.
However few, like HTMD, are built allowing scriptable system preparation for multiple hundreds of such systems.
The purpose of HTMD is to provide all tools necessary for an integrated Molecular Dynamics simulation based discovery pipeline.
Therefore, in our most recent published work (S. Doerr, T. Giorgino, G. Martinez-Rosell, J.M. Damas, G. de Fabritiis High-Throughput Automated Preparation and Simulation of Membrane Proteins with HTMD in J. Chem. Theory Comput. 2017,) we present the system building and preparation tools of HTMD and it’s application on a complex use case which is the preparation of protein-membrane systems.
We apply a single building and equilibration protocol on all eukaryotic membrane proteins of the OPM database (Orientations of Proteins in Membranes)
and perform a short equilibration runs to test for the stability of the systems.
All data from the building and equilibration runs of the OPM systems is provided to the users through a webservice which also allows direct view of the trajectories, various plots and download options for further inspection.
We believe that this and upcoming advances of HTMD will help simplifying the process of performing MD-based experiments and will further broaden the user-base and popularity of Molecular Dynamics simulations.